Stream water residence times within streambed sediments are key values to quantify hyporheic processes including sediment thermal regime, solute transient storage, dilution rates and biogeochemical transformations, such as those controlling degassing nitrous oxide. Heterogeneity of the streambed sediment hydraulic properties has been shown to be potentially an important factor to characterize hyporheic processes. Here, we quantify the importance of streambed heterogeneity on residence times of dune-like bedform induced hyporheic fluxes at the bedform and reach scales. We show that heterogeneity has a net effect of compression of the hyporheic zone (HZ) toward the streambed, changing HZ volume from the homogenous case and thus inducing remarkable differences in the flow field with respect to the homogeneous case. We unravel the physical conditions for which the commonly used homogenous field assumption is applicable for quantifying hyporheic processes thus explaining why predictive measures based on a characteristic residence time, like the Damköhler number, are robust in heterogeneous sand bedded streams.